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Authors: Claudio Slamovits, Pia Elustondo, Ronie Haro, Susana [email protected]
Group: Slamovits Lab
Summary: Map and sequence of the construct used to transform Oxyrrhis marina using electroporation.

Proper citation: Claudio Slamovits, Pia Elustondo, Ronie Haro, Susana [email protected] 2019. Om-mCherry-hsp90. protocols.io https://dx.doi.org/10.17504/protocols.io.74hhqt6 Copy   

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Authors: Guy Aidelberg, Rachel Aronoff
Group: XPRIZE Rapid Covid Testing, Guy Aidelberg
Summary: A protocol for freeze-drying (Lyophilization) of CoronaDetective tests, and more generally any QUASR RT-LAMP reaction.The amounts here are for one 96 well standard PCR plate and for reactions This can be scaled for any amount and size.

Proper citation: Guy Aidelberg, Rachel Aronoff 2020. Freeze-drying (Lyophilization) of CoronaDetective tubes. protocols.io https://dx.doi.org/10.17504/protocols.io.bk44kyyw Copy   

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Authors: Peter Vangheluwe, Sarah Van Veen
Summary: Using Ultracentrifugation, this protocol outlines the steps necessary to obtain different organelle fractions from cells.

Proper citation: Peter Vangheluwe, Sarah Van Veen 2020. Cell Fractionation. protocols.io https://dx.doi.org/10.17504/protocols.io.bazhif36 Copy   

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Authors: J Jobu Babin
Summary: This paper reports the results of an experiment involving text-messaging and emojis in laboratory trust games executed on mobile devices. Decomposing chat logs, I find that trust increases dramatically with the introduction of emojis to one-shot games, while reciprocation increases only modestly. Skin tones embeddedin emojis impact sharing and resulting gains – to the benefit of some anddetriment to others. Both light and dark skin players trust less on receipt of a dark skin tone emoji – suggestive of statistical discrimination. In this way, computer-mediated communication leads to reduced gains for dark-skinned persons. These results highlight the complex social judgment that motivates trust in an anonymous counterpart.

Proper citation: J Jobu Babin 2020. Linguistic signaling, emojis, and skin tone in trust games. protocols.io https://dx.doi.org/10.17504/protocols.io.bcvpiw5n Copy   

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Authors: James Thornton
Group: Hurwitz Lab, MetaFunc Course
Summary: The Sequence Read Archive (SRA) is a database for biological sequence data and is maintained by the National Center for Biotechnology Information (NCBI). Sequence files can be obtained by using the SRA Toolkit. This protocol provides the steps necessary to use the SRA toolkit to get sequence data in fastq format. 

Proper citation: James Thornton 2016. MG_HW2: Downloading SRA data using the SRA toolkit. protocols.io https://dx.doi.org/10.17504/protocols.io.fthbnj6 Copy   

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Authors: Antonio Hartley

Proper citation: Antonio Hartley 2018. Inmunohistoquímica rápida. protocols.io https://dx.doi.org/10.17504/protocols.io.r7sd9ne Copy   

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Authors: Bogdan Budnik, Ezra Levy, Guillaume Harmange, Nikolai Slavov
Summary: Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To alleviate these limitations, we developed Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS), and validated its ability to identify distinct human cancer cell types based on their proteomes. We used SCoPE-MS to quantify over a thousand proteins in differentiating mouse embryonic stem (ES) cells. The single-cell proteomes enabled us to deconstruct cell populations and infer protein abundance relationships. Comparison between single-cell proteomes and transcriptomes indicated coordinated mRNA and protein covariation. Yet many genes exhibited functionally concerted and distinct regulatory patterns at the mRNA and the protein levels, suggesting that post-transcriptional regulatory mechanisms contribute to proteome remodeling during lineage specification, especially for developmental genes. SCoPE-MS is broadly applicable to measuring proteome configurations of single cells and linking them to functional phenotypes, such as cell type and differentiation potentials.

Proper citation: Bogdan Budnik, Ezra Levy, Guillaume Harmange, Nikolai Slavov 2020. SCoPE-MS. protocols.io https://dx.doi.org/10.17504/protocols.io.bgt4jwqw Copy   

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Authors: Joshua Lucate
Group: Bio Basic Inc.
Summary: This protocol is for the extraction and purification of up to 10ug of plasmid DNA. It can be used for the purification of plasmid DNA ranging from 40 bp to 40kbp. 

Proper citation: Joshua Lucate 2018. Plasmid DNA miniprep protocol for EZ-10 Spin Column Plasmid DNA minipreps kit (BS413), 50 preps. protocols.io https://dx.doi.org/10.17504/protocols.io.n8tdhwn Copy   

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Authors: Integrated Islet Distribution Program
Group: Integrated Islet Distribution Program
Summary: To establish a standardized method for the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) sponsored research in the Integrated Islet Distribution Program (IIDP) for preparing a sentinel flask of human islets in order to monitor sterility and islet integrity at the production center. This is a representative sample of the islet preparation that has been distributed to investigators and is held at the distributing center as a quality control sample. The islets are cultured in the same shipping media used for islet shipment, for 18 hours at 4-8°C, simulating the cold shipping conditions followed by 2 days at 37°C culture. The flask of islets are verification in the event of a dispute over sterility or islet quality.

Proper citation: Integrated Islet Distribution Program 2020. Sentinel Flask Preparation for Cold Shipping Protocol of Human Islets. protocols.io https://dx.doi.org/10.17504/protocols.io.bhdpj25n Copy   

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Authors: Sam Li
Group: BioLegend
Summary: Product description and procedure summary: Target cells are positively selected or depleted by incubating the sample with an anti-human APC conjugated antibody, followed by incubation with magnetic anti-APC Nanobeads. The magnetically labeled fraction is retained by the use of a magnetic separator. These are the APC+ cells, do not discard them if those are the cells of interest. Some of the downstream applications include functional assays, gene expression, phenotypic characterization, etc.Note: This procedure is optimized for the isolation of 107 to 2 x 108 cells per tube. If working with fewer than 107 cells, keep volumes as indicated for 107 cells. For best results, optimize the conditions to your specific cell number and tissue. Prepare fresh MojoSort™ Buffer solution by diluting the 5X concentrate with sterile distilled water.Scale up volumes if using 14mL tubes and Magnet, and place the tube in the magnet for 10 minutes.

Proper citation: Sam Li 2019. MojoSort™ Mouse anti-APC Nanobeads Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7xhhpj6 Copy   

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Authors: Joseph Patterson, Allyson Cole-Strauss, John Beck, Caryl Sortwell, Jack Lipton
Group: Coronavirus Method Development Community
Summary: PCR based tests, such as quantitative PCR (qPCR) are the gold standard to test for the novel coronavirus (SARS-Cov2). Many labs regularly use qPCR for their own specific projects. The ability to process samples and detect SARS-Cov2 is not very different from the methods these labs are already intimately familiar with. This protocol outlines the methods that our group is using to detect SARS-Cov2 RNA in human samples.

Proper citation: Joseph Patterson, Allyson Cole-Strauss, John Beck, Caryl Sortwell, Jack Lipton 2020. Detection of Sars-Cov2 Using qPCR. protocols.io https://dx.doi.org/10.17504/protocols.io.bfaujiew Copy   

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Authors: Catherine Cesa-Luna, Alberto Aguayo-Acosta, Antonino Baez, Jesús Muñoz-Rojas, Verónica Quintero-Hernández
Summary: Inhibitory substances can be obtained and purified by different methodologies. Free cell supernatants obtained by centrifugation and filtration are commonly used for evaluating antimicrobial metabolites produced by bacteria. In this work, a new methodology for obtaining antimicrobial metabolites is proposed, especially implemented for bacteria which are not able to produce these compounds in liquid media; based on the use of nitrocellulose filter membranes and solid culture media.

Proper citation: Catherine Cesa-Luna, Alberto Aguayo-Acosta, Antonino Baez, Jesús Muñoz-Rojas, Verónica Quintero-Hernández 2020. Cold-leaching extraction. A new methodology for obtaining inhibitory substances produced by bacteria in solid media.. protocols.io https://dx.doi.org/10.17504/protocols.io.bhs3j6gn Copy   

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Authors: Barbora Lubyova

Proper citation: Barbora Lubyova 2017. PRMT5: a Novel Regulator of Hepatitis B Virus Replication and an Arginine Methylase of HBV Core. protocols.io https://dx.doi.org/10.17504/protocols.io.je8cjhw Copy   

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Authors: Curtis Huttenhower
Group: VERVE Net, Huttenhower Lab
Summary: In this protocol, we will merge the 20 profiled metagenomes in a table of relative abundances and visualize the table with a heatmap.

Proper citation: Curtis Huttenhower 2016. MetaPhlAn output merge and visualization. protocols.io https://dx.doi.org/10.17504/protocols.io.d9q95v Copy   

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Authors: Daphna Strauss, Ayelet Rahat, Israa Sharkia, Alon Chappleboim, Miriam Adam, Daniel Kitsberg, Gavriel Fialkoff, Matan Lotem, Omer Gershon, Anna-Kristina Schmidtner, Esther Oiknine-Djian, Agnes Klochendler, Ronen Sadeh, Yuval Dor, Dana Wolf, Naomi Habib, Nir Friedman
Summary: The global SARS-CoV-2 pandemic led to a steep increase in the need for viral detection tests worldwide. Most current tests for SARS-CoV-2 are based on RNA extraction followed by quantitative reverse-transcription PCR assays that involve a separate RNA extraction and qPCR reaction for each sample with a fixed cost and reaction time. While automation and improved logistics can increase the capacity of these tests, they cannot exceed this lower bound dictated by one extraction and reaction per sample. Multiplexed next generation sequencing (NGS) assays provide a dramatic increase in throughput, and hold the promise of richer information on viral strains and host immune response.Here, we establish a significant improvement of existing RNA-seq detection protocols. Our workflow, ApharSeq (Amplicon Pooling by Hybridization And RNA-Seq), includes a fast and cheap RNA capture step, that is coupled to barcoding of individual samples, followed by sample-pooling prior to the reverse transcription, PCR and massively parallel sequencing. Thus, only one step is performed before pooling hundreds of barcoded samples for subsequent steps and further analysis. Considering these improvements, our proposed workflow is estimated to reduce costs by 10-50 fold, labor by 5-100 fold, automated liquid handling by 5-10 fold, and reagent requirements by 100-1000 fold compared to existing methods.

Proper citation: Daphna Strauss, Ayelet Rahat, Israa Sharkia, Alon Chappleboim, Miriam Adam, Daniel Kitsberg, Gavriel Fialkoff, Matan Lotem, Omer Gershon, Anna-Kristina Schmidtner, Esther Oiknine-Djian, Agnes Klochendler, Ronen Sadeh, Yuval Dor, Dana Wolf, Naomi Habib, Nir Friedman 2020. SARS-CoV-2 detection with ApharSeq. protocols.io https://dx.doi.org/10.17504/protocols.io.bjgukjww Copy   

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Authors: David Kotol
Group: Human Cell Atlas Method Development Community, Human Protein Atlas
Summary: Here, a workflow for sample preparation and quantification of brain and pancreatic tissue proteins with use of heavy labelled protein standards (QPrESTs) is described. The standards are added before the digestion ensuring high reproducibility and elimination of nuances apearing during proteolytical cleavage of proteins and further steps such as solid phase extraction. QPrESTs are heavy labelled recombinant protein fragments covering regions of proteins with low homology and span over 50-150 aminoacids. They were produced as a part of Human Protein Atlas project in auxotrofic E.coli and individually purified, serving as an excelent resource for MS-based protein quantification.

Proper citation: David Kotol 2019. Tissue lysis and digestion for MS analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.yguftww Copy   

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Authors: Leila Pishevar

Proper citation: Leila Pishevar 2017. Effect of food simulating liquids on the flexural strength of the methacrylate and silorane-based composites. protocols.io https://dx.doi.org/10.17504/protocols.io.icbcasn Copy   

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Authors: Qi Y

Proper citation: Qi Y 2019. Sample Preparation for Western Blot. protocols.io https://dx.doi.org/10.17504/protocols.io.z7xf9pn Copy   

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Authors: Kiichi Hirota

Proper citation: Kiichi Hirota 2019. Western blot analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.x9mfr46 Copy   

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Authors: Mauricio Durigan
Summary: This is the protocol for the touchdown PCR assay

Proper citation: Mauricio Durigan 2018. TOUCHDOWN PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.nyzdfx6 Copy   

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